9JUI

Crystal structure of FFAT motif of Nir2 bound to VAPB

Summary for 9JUI

• Entry DOI: 10.2210/pdb9jui/pdb
• Descriptor: Vesicle-associated membrane protein-associated protein B, Nir2 FFAT motif, ZINC ION, ... (4 entities in total)
• Functional Keywords: plc signaling, pi cycle, membrane contact site, lipid transfer, lipid binding, lipid binding protein
• Biological source: Mus musculus (house mouse); More
• Total number of polymer chains: 2
• Total formula weight: 16074.29

Authors

Kim, D.,Lee, C. (deposition date: 2024-10-08, release date: 2025-10-15, Last modification date: 2025-11-05)

Primary citation

Kim, D.,Lee, S.,Jun, Y.,Lee, C.
Nir2 crystal structures reveal a phosphatidic acid-sensing mechanism at ER-PM contact sites.
Proc.Natl.Acad.Sci.USA, 122:e2516849122-e2516849122, 2025

PubMed Abstract: Agonist-induced activation of phosphoinositide-specific phospholipase C (PLC) converts phosphatidylinositol 4,5-bisphosphate [PI(4,5)P] to diacylglycerol (DAG) at the inner leaflet of the plasma membrane (PM). DAG can be enzymatically transformed into phosphatidic acid (PA) and accumulated at the PM. PYK2 N-terminal domain-interacting receptor 2 (Nir2) mediates the formation of ER-PM membrane contact sites (MCSs) by specifically recognizing PA at the PM and directly interacting with ER membrane protein vesicle-associated membrane protein-associated proteins (VAPs). The N-terminal phosphatidylinositol transfer protein domain of Nir2 facilitates PI/PA exchange at ER-PM MCSs to maintain PI and PA levels. Here, we reveal the mechanisms by which Nir2 senses phosphatidic acid (PA) and associates with membranes, based on three crystal structures of its C-terminal Lipin/Ned1/Smp2 (LNS2) domain bound to PA, the diphenylalanine [FF]-containing acidic tract (FFAT) motif complexed with vesicle-associated membrane protein-associated protein B/C (VAPB), and the Asp-Asp-His-Asp (DDHD) domain. The C-terminal LNS2 domain of Nir2 directly interacts with the phosphate in the headgroup of PA via hydrogen bonds involving S1025, T1065, K1103, and K1126. Formation of a salt bridge between E355 in Nir2 and R55 in VAPB is essential for Nir2 FFAT-VAPB interaction. The central DDHD domain of Nir2 forms a twofold symmetric dimer, and this self-association contributes to stable and tight membrane association. These findings reveal how Nir2-mediated ER-PM MCS formation maintains continued PI(4,5)P-dependent PLC signaling.

PubMed: 41129229
DOI: 10.1073/pnas.2516849122

Experimental method

X-RAY DIFFRACTION (2.05 Å)